Package ffx.algorithms.cli

Class AnnealOptions

java.lang.Object

ffx.algorithms.cli.AnnealOptions

public class AnnealOptions
extends Object

Represents command line options for scripts that utilize simulated annealing.

Since:

1.0

Author:

Michael J. Schnieders, Jacob M. Litman

Constructor Summary

Constructors

Constructor	Description
AnnealOptions()

Method Summary

Modifier and Type	Method	Description
SimulatedAnnealing	createAnnealer(DynamicsOptions dynamicsOptions, MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener)	Creates a SimulatedAnnealing object.
SimulatedAnnealing	createAnnealer(DynamicsOptions dynamicsOptions, MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener, File dynFile)	Creates a SimulatedAnnealing object.
double	getLow()	Low temperature limit in degrees Kelvin.
AnnealingSchedule	getSchedule()	Constructs an AnnealingSchedule.
int	getTemperAfter()	Sets the number of annealing windows to hold flat at the low temperature (in addition to normal windows).
int	getTemperBefore()	Sets the number of annealing windows to hold flat at the high temperature (in addition to normal windows).
String	getTemperString()	Sets the schedule to be used.
double	getUpper()	Upper temperature limit in degrees Kelvin.
int	getWindows()	Number of annealing windows.
boolean	isReinitVelocities()	Forces simulated annealing to re-initialize velocities to the new temperature at each annealing step, rather than letting the thermostat shift temperature downwards.
void	setLow(double low)
void	setReinitVelocities(boolean reinitVelocities)
void	setTemperAfter(int temperAfter)
void	setTemperBefore(int temperBefore)
void	setTemperString(String temperString)
void	setUpper(double upper)
void	setWindows(int windows)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

AnnealOptions

public AnnealOptions()

Method Details

getWindows

public int getWindows()

Number of annealing windows.

Returns:

Returns the number of windows.

createAnnealer

public SimulatedAnnealing createAnnealer(DynamicsOptions dynamicsOptions,
 MolecularAssembly molecularAssembly,
 Potential potential,
 AlgorithmListener algorithmListener)

Creates a SimulatedAnnealing object.

Parameters:

dynamicsOptions - Dynamics options to use.

molecularAssembly - MolecularAssembly

potential - Potential

algorithmListener - AlgorithmListener

Returns:

SimulatedAnnealing

createAnnealer

public SimulatedAnnealing createAnnealer(DynamicsOptions dynamicsOptions,
 MolecularAssembly molecularAssembly,
 Potential potential,
 AlgorithmListener algorithmListener,
 File dynFile)

Creates a SimulatedAnnealing object.

Parameters:

dynamicsOptions - Dynamics options to use.

molecularAssembly - MolecularAssembly

potential - Potential

algorithmListener - AlgorithmListener

dynFile - Dynamics restart file.

Returns:

SimulatedAnnealing

getSchedule

public AnnealingSchedule getSchedule()

Constructs an AnnealingSchedule.

Returns:

An AnnealingSchedule.

setWindows

public void setWindows(int windows)

getLow

public double getLow()

Low temperature limit in degrees Kelvin.

Returns:

Returns the low temperature limit.

setLow

public void setLow(double low)

getUpper

public double getUpper()

Upper temperature limit in degrees Kelvin.

Returns:

Returns the upper temperature limit.

setUpper

public void setUpper(double upper)

isReinitVelocities

public boolean isReinitVelocities()

Forces simulated annealing to re-initialize velocities to the new temperature at each annealing step, rather than letting the thermostat shift temperature downwards.

Returns:

Returns true for re-initialization of velocities.

setReinitVelocities

public void setReinitVelocities(boolean reinitVelocities)

getTemperString

public String getTemperString()

Sets the schedule to be used.

Returns:

Returns a String representation of the tempering schedule.

setTemperString

public void setTemperString(String temperString)

getTemperBefore

public int getTemperBefore()

Sets the number of annealing windows to hold flat at the high temperature (in addition to normal windows).

Returns:

Returns the number of annealing windows to hold flat at the high temperature.

setTemperBefore

public void setTemperBefore(int temperBefore)

getTemperAfter

public int getTemperAfter()

Sets the number of annealing windows to hold flat at the low temperature (in addition to normal windows).

Returns:

Returns the number of annealing windows to hold flat at the low temperature.

setTemperAfter

public void setTemperAfter(int temperAfter)